Frequently asked questions

What is the Cyclodextrin Knowledgebase?

Cyclodextrin Knowledgebase is a publicly available and easily usable complex knowledgebase platform that gathers relevant information on cyclodextrin complexation. This is the most comprehensive database on cyclodextrin complexation available on web. The database contains four modules: Publication, Interaction, Chirality and Analysis modules. In the Publication module, almost fifty-thousand publication details are collected that can be retrieved by text search. In the Interaction and Chirality Modules relevant literature data on cyclodextrin complexation and chiral recognition are collected that can be retrieved by both text and structural search. In the Analysis Module, geometry of small molecule-cyclodextrin complexes can be predicted using molecular docking tools in order to explore the geometry and interaction energy of the inclusion complexes.

Who is allowed to use the Cyclodextrin Knowledgebase?

Because it is freely accessible at our website (http://www.cyclodextrin.net) any individual interested in cyclodextrin complexation can use it without limitation.

Do I need to register for using Cyclodextrin Knowledgebase?

No, there is no need to register, so everyone can use it anonymously. In this case one should login with a user name cycloguest using password cyclo. However, one can register and have his/her on account.

What kind of programs should I have on my PC?

Cyclodextrin Knowledgebase has the users web browser on the client side. These html-based web interfaces were tested using Internet Explorer and Mozilla Firefox.

What does the Cyclodextrin Knowledgebase architecture look like?

The core of the Cyclodextrin Knowledgebase web application is our integrating PHP software connected to a MySQL relational database, where the different tasks are automatically managed by daemons running on our servers. The MySQL database plays a central role in storing all pieces of information required for the application to fully function, e.g. molecular data of cyclodextrins, ligands, etc. The input data is read from the database and output data is directed into the database. Besides, the powerful web application Zend Framework is incorporated. It allows easy, fast and robust web development by leveraging the Model-View-Controller (MVC) paradigm. It also provides components for the MVC, Row Data Gateway or Table Data Gateway design patterns. For chemical structure drawing Marvin Sketch (Chemaxon, http://www.chemaxon.com) is provided for users to draw a small molecule structure, or alternatively, to upload a ligand structure file most popular formats (e.g. mol; mol2; pdb). For chemistry file format conversion (Open Babel 2.2.3 www.openbabel.org) is used. Two-dimensional (2D) and three-dimensional (3D) molecule structures are represented by Marvin View. Generated by molecular docking, CD-ligand complexes are rendered by VMD [7]. Jchem engine, a collection of programs and toolkits for many tasks (Chemaxon, http://www.chemaxon.com) is applied for structure search by means of calculation dissimilarity coefficients of molecular descriptors using Tanimoto metrics. In Analysis Module docking calculations are performed using AutoDock 4.2, allowing docking of flexible ligands to cyclodextrins. The calculations are performed using a distance-dependent dielectric function to model solvent. The inventory of incorporated software is given below.

Tool Description
Apache HTTP server for load balancing
MySQL SQL server
Babel File format converter in chemistry
Jmol 3D molecular viewer
Chemaxon Marvin Ligand structure sketching and editing
Chemaxon Jchem Ligand physico/chemical property calculation
Autodock Software for molecular docking calculation
MOPAC2009 Semi-empirical quantum chemical software for calculation of partial charges

How to use Publication Module?

Publication database module contains almost 50,000 entries. Using this module, a text search in the database can be carried out by keywords in title, by author(s) and year of publication. In addition, for many entries a link to the publication is given. Furthermore, where possible a link to the Knowledgebases Interaction module is provided.

May I perform structure search in Publication Module?

No, this module is designed for text search only.

How to use Interaction Module?

This module contains above 10,000 entries. It provides structural search within the database being the most straightforward technique of data mining. The chemical structure of the compound of interest can be drawn in and either substructure (the retrieval of all molecules that contain the query substructure) or similarity search (finding the compounds that are most similar to the query) can be carried out. The result output provides the list of interactions that meet the query. An interaction entry contains the structure of the complexing ligand, with its empirical formula and molecular mass, the name and structure of the interacting cyclodextrin with its physical properties (formula, average molecular mass) as well as -where available-the binding constant and experimental details such as the method of determination including the temperature and pH. This module provides direct link to the publication source.

How to use Chirality Module?

The usage is of this module (containing above 5,000 entries) is identical to that of Interaction Module. What is the difference between Interaction and Chirality Modules? Interaction module contains publications dealing with inclusion complexes, whereas in Chirality Module publications that have the topic of chiral recognition are included.

What is the Analysis Module for?

When no data is available in the literature concerning a given cyclodextrin-ligand complexation it can be used to get a hint regarding the complex geometry and interaction energy.

What kind of procedure is used in the Analysis Module?

In this module molecular docking tools are used.

Do I need experience in molecular docking for using the Analysis Module?

No, this module offers our web-based interface that handles all aspects molecular docking procedure. It integrates a number of computational chemistry software specifically aimed at correctly calculating parameters needed at different steps of the docking procedure, i.e. docking calculation, descriptor calculation and cyclodextrin-ligand complex representation.

How many cyclodextrin structures are incorporated into the Analysis Module?

Three dimensional structures of ACD, BCD, GCD and 95 cyclodextrin derivatives were built based on the crystal structures of parent cyclodextrins are offered for molecular docking calculations. The optimized structure and partial charges of cyclodextrins were calculated at a given pH using molecular mechanics (MMFF94) and semi-empirical quantum mechanical (PM6) methods.

How to use Analysis Module?

The query compound can be drawn in (or imported) into a Marvin applet and then the structure is automatically set up for docking calculations. After selecting (up to 5) cyclodextrin molecules, docking calculations is performed, resulting in docking energies, docking geometries and interaction surfaces of the calculated complexes. Three dimensional figures of the calculated ligand-cyclodextrin complexes are generated, thus it can be visually inspected in detail. In addition, calculated docking energies and contact surfaces are also given.

May I print out the results of my query?

Yes, the results can be printed out.

May I download the results of my query?

Yes, all results (both textual and graphic) may be downloaded.

Does anyone access to my data?

No, if you are a registered user.